Gunjan, this may be related to an Ubuntu specific issue we address on the Freesurfer download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download Specifically the part thats states the following: *** On Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3 *** -Zeke On 11/18/2014 03:55 AM, Gunjan Gautam wrote: > Hello Sir, > > I have place the "license.txt" in the same directory that contains > build-stamp.txt as there were no directory with name "FREESURFER_HOME". > freeview command is not working and showing below message > "freeview.bin: error while loading shared libraries: libjpeg.so.62: > cannot open shared object file: No such file or directory". > What next I need to do in order to generate a output brain mask. > > Best Regards, > Gunjan > > > > On Thu, Nov 13, 2014 at 12:24 AM, Z K <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: > > Im having a little difficulty following all the avenues of your attempts > to get this working, but the bottom line is that the error message below > is complaining that you do not have a valid license file. > > You need to go to this page and register and get the valid license file: > > https://surfer.nmr.mgh.harvard.edu/registration.html > > Once you get a valid license file you will need to place it in your > $FREESURFER_HOME directory (the same directory that contains > build-stamp.txt) and give it the name .license or license.txt. Try both. > > -Zeke > > On 11/12/2014 01:29 PM, Gunjan Gautam wrote: > > Sir earlier I was trying to use FreeSurfer using Virtual Box in my > > Windows machine. There the mri_convert command did not work so I > > switched to a Linux machine. Now, I'm using centos6_x86_64 version as my > > machine has the Ubuntu 12.04 platform and here also facing the same > > problem. > > > > I want to share one thing that in my institute I tried hard to download > > FreeSurfer but every time it resulted into a time-out situation so I had > > to ask someone to get it downloaded and send me through Google drive. > > This was how I installed it in my system. > > > > Best regards, > > Gunjan > > > > On Nov 12, 2014 9:15 PM, "Z K" <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu> > > <mailto:zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu>>> > wrote: > > > > Gunjan, > > > > Are you using your own version of VirtualBox, with freesurfer > installed > > on it by you? Or the VirtualBox version of freesurfer made by us and > > downloaded from our website? I am confused because in your email > below, > > freesurfer appears to be installed on the Desktop whereas the > > prepackaged version made by us is installed in /usr/local > > > > -Zeke > > > > On 11/12/2014 08:54 AM, Gunjan Gautam wrote: > > > Hello Sir, > > > > > > License file is present in the folder but with the name LICENSE. > > Should > > > I download it again ? > > > > > > Best Regards, > > > Gunjan > > > > > > On Nov 12, 2014 7:01 PM, "Bruce Fischl" > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> > > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>>> wrote: > > > > > > Hi Gunjan > > > > > > do you have a license? If not you need to download and > install it > > > (as noted in the error message). They are free. > > > > > > cheers > > > Bruce > > > On Wed, 12 Nov 2014, Gunjan Gautam wrote: > > > > > > > > > Hello Sir, > > > > > > I'm using FreeSurfer through Virtual Box. I tried > the below > > > command for > > > reslicing my volume according to a reference > volume but the > > > process gets > > > stuck at " reading volume". > > > > > > mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz > > > > > > A: Volume to be resampled / resliced > > > B: Reference Volume > > > > > > Error message is being shown like below: > > > > > > mri_convert a.nii a.resliced.nii -rl b.nii > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > > mreuter Exp $ > > > reading from a.nii... > > > > > > > ------------------------------__------------------------------__-------------- > > > ERROR: Invalid FreeSurfer license key found in > license file > > > > /home/bibl04/Data_Home/__Desktop/freesurfer/license.txt > > > If you are outside the NMR-Martinos Center, > > > go to http://surfer.nmr.mgh.harvard.__edu > > > <http://surfer.nmr.mgh.harvard.edu> to > > > get a valid license file (it's free). > > > If you are inside the NMR-Martinos Center, > > > make sure to source the standard environment. > > > > > > Actually, I have two volumes, belong to the same > subject. One > > > volume is the > > > ground truth which will be considered as standard > for the > > second > > > volume > > > which is the processed one or the extracted brain. To > > perform a > > > perfect > > > comparison between both volumes, these must > generate equal > > > number of slices > > > in order to compare the corresponding slide. But here > > there is > > > problem with > > > my volumes, that is while performing slicing > Ground Truth > > volume is > > > generating 360 slice and processed volume is > generating 181 > > > slides. So > > > comparison can't take place in this way. > > > > > > What all I need is to do the resampling or > generating the 181 > > > slides from > > > the Ground Truth as well. > > > > > > > > > Best Regards, > > > Gunjan > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the > person to > > > whom it is > > > addressed. If you believe this e-mail was sent to you in > > error and > > > the e-mail > > > contains patient information, please contact the Partners > > Compliance > > > HelpLine at > > >http://www.partners.org/complianceline . If the e-mail was sent to > > > you in error > > > but does not contain patient information, please contact the > > sender > > > and properly > > > dispose of the e-mail. > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > >Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
